Shown here is a circular diagram generated using the
FR3D annotations
for 9S3D. The black circle represents the annotated chains. For
some structures an airport diagram is provided. To draw it click the
airport button. Structures without one have a disabled button.
Interactions
Interactions are displayed as arcs connecting nucleotides,
by default only cWW interactions are displayed. The
dotted arcs
are long range interactions, there include things like
pseudoknots. To display other interactions use the interaction
controls to the right. Clicking on a interaction will toggle
displaying all interactions of that family and ones near that
family. So clicking on tWW shows all tWW and ntWW.
Motifs
In airport mode motifs are displayed by default. To hide them click the motif button.
Internal loops are shown in a green box, hairpins in blue and 3-way junctions in yellow.
Currently we only extract 3-way junctions, in the future this may change.
Modes
In the default select mode, click and drag to create a selection box.
All nucleotides within the selection box will be displayed in a jmol
window to the right. The selection box is dragable and resizeable.
In click mode, click on a interaction or nucleotide to display it
in 3D. In addition, some information about the clicked element will
be displayed below the jmol window. To switch to the click mode use
the selection mode control. Hovering over an interaction will
highlight it and the nucleotides that form it. Hovering over a
nucleotide will highlight it as well as all intereracations it forms.
More details